add Sys.sleep(1) to test_inits and remove capture.output

tests/testthat/test-fit-init.R

@@ -1,110 +1,133 @@
 context("fitted-inits")
 set_cmdstan_path()
 
-mod_params <- testing_model("parameter_types")
-mod_schools <- testing_model("schools")
-mod_logistic <- testing_model("logistic")
-mod_logistic_simple <- testing_model("logistic_simple")
+
 data_list_schools <- testing_data("schools")
 data_list_logistic <- testing_data("logistic")
 test_inits <- function(mod, fit_init, data_list = NULL) {
-  utils::capture.output(fit_sample <- mod$sample(data = data_list, chains = 1,
-                                                 init = fit_init, iter_sampling = 100, iter_warmup = 100, refresh = 0,
-                                                 seed = 1234))
-  utils::capture.output(fit_sample <- mod$sample(data = data_list, chains = 5,
-                                                 init = fit_init, iter_sampling = 100, iter_warmup = 100, refresh = 0,
-                                                 seed = 1234))
-  utils::capture.output(fit_vb <- mod$variational(data = data_list, refresh = 0,
-                                                  seed = 1234, init = fit_init, algorithm = "fullrank"))
-  utils::capture.output(fit_path <- mod$pathfinder(data = data_list, seed=1234,
-                                                   refresh = 0, num_paths = 4, init = fit_init))
-  utils::capture.output(fit_laplace <- mod$laplace(data = data_list,
-                                                   seed = 1234, refresh=0, init=fit_init))
-  utils::capture.output(fit_ml <- mod$optimize(data = data_list, seed = 1234,
-                                               refresh = 0, init = fit_init, history_size = 400, jacobian = TRUE,
-                                               algorithm = "lbfgs", tol_param = 1e-12, tol_rel_grad = 1e-12,
-                                               tol_grad = 1e-12, tol_rel_obj = 1e-12, tol_obj = 1e-12, init_alpha = 1e-4,
-                                               iter = 400))
-  draws = posterior::as_draws_rvars(fit_sample$draws())
-  utils::capture.output(fit_sample <- mod$sample(data = data_list, chains = 1,
-                                                 init = draws, iter_sampling = 100, iter_warmup = 100, refresh = 0,
-                                                 seed = 1234))
+  Sys.sleep(1)
+  fit_sample <- mod$sample(data = data_list, chains = 1, init = fit_init,
+    iter_sampling = 100, iter_warmup = 100, refresh = 0, seed = 1234)
+  Sys.sleep(1)
+  fit_sample_multi <- mod$sample(data = data_list, chains = 5, init = fit_init,
+    iter_sampling = 100, iter_warmup = 100, refresh = 0, seed = 1234)
+  Sys.sleep(1)
+  fit_vb <- mod$variational(data = data_list, refresh = 0, seed = 1234,
+    init = fit_init, algorithm = "fullrank")
+  Sys.sleep(1)
+  fit_path <- mod$pathfinder(data = data_list, seed=1234, refresh = 0,
+    num_paths = 4, init = fit_init)
+  Sys.sleep(1)
+  fit_laplace <- mod$laplace(data = data_list, seed = 1234, refresh=0,
+    init=fit_init)
+  Sys.sleep(1)
+  fit_ml <- mod$optimize(data = data_list, seed = 1234, refresh = 0,
+    init = fit_init, history_size = 400, algorithm = "lbfgs")
+  Sys.sleep(1)
+  draws = posterior::as_draws_rvars(fit_init$draws())
+  fit_sample_draws <- mod$sample(data = data_list, chains = 1, init = draws,
+    iter_sampling = 100, iter_warmup = 100, refresh = 0, seed = 1234)
+  Sys.sleep(1)
   return(0)
 }
 
 test_that("Sample method works as init", {
   set.seed(1234)
+  mod_params <- testing_model("parameter_types")
   utils::capture.output(fit_sample_init <- mod_params$sample(chains = 1,
     iter_warmup = 100, iter_sampling = 100, refresh = 0, seed = 1234))
-  utils::capture.output(fit_sample_multi_init <- mod_params$sample(chains = 4, init = fit_sample_init,
-    iter_warmup = 100, iter_sampling = 100, refresh = 0, seed = 1234))
   expect_no_error(test_inits(mod_params, fit_sample_init))
+})
+
+test_that("Multi chain Sample method works as init", {
+  set.seed(1234)
+  mod_params <- testing_model("parameter_types")
+  utils::capture.output(fit_sample_multi_init <- mod_params$sample(chains = 4,
+    iter_warmup = 100, iter_sampling = 100, refresh = 0, seed = 1234))
   expect_no_error(test_inits(mod_params, fit_sample_multi_init))
 })
 
 test_that("Subsets of parameters are allowed", {
   set.seed(1234)
+  mod_logistic_simple <- testing_model("logistic_simple")
   utils::capture.output(fit_sample_init_simple <- mod_logistic_simple$sample(chains = 1,
     data = data_list_logistic, iter_warmup = 100, iter_sampling = 100,
     refresh = 0, seed = 1234))
-  expect_message(test_inits(mod_logistic, fit_sample_init_simple,
+  mod_logistic <- testing_model("logistic")
+  expect_no_error(test_inits(mod_logistic, fit_sample_init_simple,
     data_list_logistic))
 })
 
+test_that("Pathfinder works as init", {
+  mod_logistic <- testing_model("logistic")
+  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(
+    seed=1234, data = data_list_logistic, refresh = 0, num_paths = 1))
+  expect_no_error(test_inits(mod_logistic, fit_path_init, data_list_logistic))
+})
 
-test_that("Pathfinder method works as init", {
+test_that("Multi Pathfinder method works as init", {
   set.seed(1234)
-  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234, data = data_list_logistic,
-                                                               refresh = 0, num_paths = 4))
-  expect_no_error(test_inits(mod_logistic, fit_path_init,
-    data_list_logistic))
-  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234, data = data_list_logistic,
-                                                               refresh = 0, num_paths = 1))
-  expect_no_error(test_inits(mod_logistic, fit_path_init,
-    data_list_logistic))
+  mod_logistic <- testing_model("logistic")
+  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234,
+    data = data_list_logistic, refresh = 0, num_paths = 4))
+  expect_no_error(test_inits(mod_logistic, fit_path_init, data_list_logistic))
 })
 
 test_that("Pathfinder method with psis_resample as false works as init", {
   set.seed(1234)
-  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234, data = data_list_logistic,
-    refresh = 0, num_paths = 4, psis_resample = FALSE))
-  expect_no_error(test_inits(mod_logistic, fit_path_init,
-    data_list_logistic))
-  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234, data = data_list_logistic,
-    refresh = 0, num_paths = 1))
-  expect_no_error(test_inits(mod_logistic, fit_path_init,
-    data_list_logistic))
+  mod_logistic <- testing_model("logistic")
+  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(
+    seed=1234, data = data_list_logistic, refresh = 0, num_paths = 1))
+  expect_no_error(test_inits(mod_logistic, fit_path_init, data_list_logistic))
 })
 
-test_that("Pathfinder method with calculate_lp as false works as init", {
+test_that("Multi Pathfinder method with psis_resample as false works as init", {
   set.seed(1234)
-  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234, data = data_list_logistic,
-    refresh = 0, num_paths = 4, psis_resample = TRUE, calculate_lp = FALSE))
-  expect_no_error(test_inits(mod_logistic, fit_path_init,
-    data_list_logistic))
-  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(seed=1234, data = data_list_logistic,
-    refresh = 0, num_paths = 1))
-  expect_no_error(test_inits(mod_logistic, fit_path_init,
-    data_list_logistic))
+  mod_logistic <- testing_model("logistic")
+  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(
+    seed=1234, data = data_list_logistic, refresh = 0, num_paths = 4,
+    psis_resample = FALSE))
+  expect_no_error(test_inits(mod_logistic, fit_path_init, data_list_logistic))
 })
 
 test_that("Laplace method works as init", {
   set.seed(1234)
+  mod_logistic <- testing_model("logistic")
   utils::capture.output(fit_laplace_init <- mod_logistic$laplace(
     data = data_list_logistic, seed = 1234, refresh=0))
   expect_no_error(test_inits(mod_logistic, fit_laplace_init,
-                             data_list_logistic))
+    data_list_logistic))
+})
+
+test_that("Pathfinder method with calculate_lp as false works as init", {
+  set.seed(1234)
+  mod_logistic <- testing_model("logistic")
+  fit_path_init <- mod_logistic$pathfinder(
+    seed=1234, data = data_list_logistic, refresh = 0, num_paths = 1,
+    psis_resample = FALSE, calculate_lp = FALSE)
+  expect_no_error(test_inits(mod_logistic, fit_path_init, data_list_logistic))
+})
+
+test_that("Multi Pathfinder method with calculate_lp as false works as init", {
+  set.seed(1234)
+  mod_logistic <- testing_model("logistic")
+  utils::capture.output(fit_path_init <- mod_logistic$pathfinder(
+    seed=1234, data = data_list_logistic, refresh = 0, num_paths = 4,
+    psis_resample = TRUE, calculate_lp = FALSE))
+  expect_no_error(test_inits(mod_logistic, fit_path_init, data_list_logistic))
 })
 
 test_that("Variational method works as init", {
   set.seed(1235)
+  mod_logistic <- testing_model("logistic")
   utils::capture.output(fit_vb_init <- mod_logistic$variational(
     data = data_list_logistic, seed=1234, refresh = 0))
   expect_no_error(test_inits(mod_logistic, fit_vb_init, data_list_logistic))
 })
 
 test_that("Optimization method works as init", {
   set.seed(1234)
+  mod_logistic <- testing_model("logistic")
   utils::capture.output(fit_ml_init <- mod_logistic$optimize(
     data = data_list_logistic, seed=1234, refresh = 0))
   expect_no_error(test_inits(mod_logistic, fit_ml_init, data_list_logistic))
@@ -113,6 +136,7 @@ test_that("Optimization method works as init", {
 
 test_that("Draws Object with NA or Inf throws error", {
   set.seed(1234)
+  mod_logistic <- testing_model("logistic")
   utils::capture.output(fit_laplace_init <- mod_logistic$laplace(
     data = data_list_logistic, seed = 1234, refresh=0))
   draws_df = fit_laplace_init$draws()